library(tidyverse)
## -- Attaching packages --------------------------------------------------------------------------------------------- tidyverse 1.3.0 --
## v ggplot2 3.3.2 v purrr 0.3.4
## v tibble 3.0.3 v dplyr 1.0.2
## v tidyr 1.1.2 v stringr 1.4.0
## v readr 1.3.1 v forcats 0.5.0
## -- Conflicts ------------------------------------------------------------------------------------------------ tidyverse_conflicts() --
## x dplyr::filter() masks stats::filter()
## x dplyr::lag() masks stats::lag()
library(sf)
## Linking to GEOS 3.8.0, GDAL 3.0.4, PROJ 6.3.1
library(gganimate)
data <- read_csv("../sgene_dropout_data/data.csv")
## Parsed with column specification:
## cols(
## week_specimen = col_date(format = ""),
## nhser_name = col_character(),
## utla_name = col_character(),
## utla_code = col_character(),
## week_infection = col_date(format = ""),
## prop_sgtf = col_double(),
## samples = col_double()
## )
geo <- read_sf("./Counties_and_Unitary_Authorities__April_2019__Boundaries_EW_BUC-shp/Counties_and_Unitary_Authorities__April_2019__Boundaries_EW_BUC.shp")
both<- inner_join(geo,data,by=c("CTYUA19NM"="utla_name")) %>% filter(week_specimen>lubridate::ymd("2020-11-1"))
a<-ggplot(both,aes(fill=prop_sgtf))+geom_sf()+scale_fill_viridis_c(option='magma',direction=-1,limits=c(0,1))+theme_minimal()+transition_time(week_specimen)+labs(title="Date: {frame_time}",fill="SGTF")
animate(a,nframes=100,height=600,width=600,fps=10,end_pause = 20)

anim_save('uksgtf.gif')